According to CS Machogu, the new directive classifies schools as independent audit units accountable to Parliament.
Machogu noted that the ministry has prescribed the maximum allowable fees to charge at each level so schools must "strictly adhere to prevailing policies and guidelines regarding illegal levies."
KPSA chairman Charles Ochome said the association is ready to work with the state to enhance educational opportunities.
MPs had voiced concerns over parents incurring transactional charges saying this will add more burden to them.
According to the PS, 12 institutions under the State Department for Basic Education have already integrated with the eCitizen platform, offering 160 services.
He emphasized the real-time accountability aspect of the system, saying it ensures schools receive the funds promptly for their operations.
This comes after the High Court on Tuesday extended orders blocking the government from collecting school fees via the eCitizen platform.
Judge Mwita noted that the government will not suffer any prejudice if the orders are extended to April 17.
The High Court on Wednesday suspended the implementation of the new payment process, pending its determination.
The interim conservatory order suspended a circular that Education Principal Secretary Belio Kipsang on January 31, 2024, ordering all fee payments to be made through the eCitizen.
The PS said the school heads will be able to access all the funds on the digital platform.
Sossion noted that the eCitizen is configured to promote transparency and eliminate all forms of corruption, allowing the government to track and account for all the funds it collects.
School heads have been ordered to provide all their institutions' bank account details by February 6, 2024.
He called on education stakeholders across the country to bring such cases to his attention.
The DP said the government has disbursed capitation funds to schools, and no teacher should send a student home for any reason.
The New Year dawned on Eastleigh like a hesitant sunrise, peeking through the haze of financial anxieties that clung to the streets like dust. 2023 had been a year of tight belts and furrowed brows.